Starting phenix.real_space_refine
on Thu Mar 13 03:21:08 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/6wb1_21584/03_2025/6wb1_21584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wb1_21584/03_2025/6wb1_21584.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2025/6wb1_21584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2025/6wb1_21584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2025/6wb1_21584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2025/6wb1_21584.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      72      5.49       5
     S       5      5.16       5
     C    5029      2.51       5
     N    1444      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8235
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 705
          Classifications: {'RNA': 33}
          Modifications used: {'5*END': 1, 'rna3p_pur': 19, 'rna3p_pyr': 13}
          Link IDs: {'rna3p': 32}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 880
          Inner-chain residues flagged as termini: ['pdbres="  G D  46 "']
          Classifications: {'DNA': 4, 'RNA': 38}
          Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21}
          Link IDs: {'rna3p': 41}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 3716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 3716
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 196}
          Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 507}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 716
          Unresolved non-hydrogen angles: 883
          Unresolved non-hydrogen dihedrals: 575
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 40, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 397
    Chain: "B"
      Number of atoms: 2934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2934
          Classifications: {'peptide': 402}
          Incomplete info: {'truncation_to_alanine': 107}
          Link IDs: {'PTRANS': 30, 'TRANS': 371}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 396
          Unresolved non-hydrogen angles: 488
          Unresolved non-hydrogen dihedrals: 323
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 27, 'ASP:plan': 11}
          Unresolved non-hydrogen planarities: 228
  Time building chain proxies: 5.84, per 1000 atoms: 0.71
  Number of scatterers: 8235
  At special positions: 0
  Unit cell: (99.64, 97.52, 119.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       5     16.00
     P      72     15.00
     O    1685      8.00
     N    1444      7.00
     C    5029      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 900.1 milliseconds
  

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1782

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      39.2% alpha, 7.0% beta
      38 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 2.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 44
      removed outlier: 3.706A  pdb=" N   ALA A  33 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.611A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.745A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 211
      removed outlier: 3.558A  pdb=" N   HIS A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 269
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 363 through 383
      removed outlier: 3.624A  pdb=" N   GLN A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
      removed outlier: 3.693A  pdb=" N   TRP A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.600A  pdb=" N   ASP A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 3.542A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
      removed outlier: 3.591A  pdb=" N   ASN A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LYS A 527 " --> pdb=" O   GLU A 523 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LYS A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'B' and resid 27 through 44
      removed outlier: 4.051A  pdb=" N   ALA B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLU B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 91
      removed outlier: 6.232A  pdb=" N   ASP B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   PHE B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 103
      removed outlier: 3.751A  pdb=" N   LYS B 101 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.810A  pdb=" N   ALA B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 154 through 175
      removed outlier: 3.553A  pdb=" N   ALA B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.772A  pdb=" N   LYS B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLN B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 211
    Processing helix  chain 'B' and resid 253 through 268
    Processing helix  chain 'B' and resid 276 through 284
      removed outlier: 3.509A  pdb=" N   LYS B 281 " --> pdb=" O   ARG B 277 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 312
      removed outlier: 3.725A  pdb=" N   GLU B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 384
      removed outlier: 3.738A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.839A  pdb=" N   TRP B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 427
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107
      removed outlier: 3.893A  pdb=" N   GLY A 190 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL A 179 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 351
      removed outlier: 6.884A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ALA A 327 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362
      removed outlier: 3.714A  pdb=" N   LYS A 512 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441
      removed outlier: 6.283A  pdb=" N   PHE A 440 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 443 through 444
      removed outlier: 4.028A  pdb=" N   ASP A 443 " --> pdb=" O   GLY A 456 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLY A 456 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49
      removed outlier: 3.792A  pdb=" N   ILE B 142 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE B 132 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE B 130 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 107
    Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 181
      removed outlier: 3.847A  pdb=" N   TYR B 181 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 350
      removed outlier: 7.107A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   THR B 338 " --> pdb=" O   GLN B 330 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN B 330 " --> pdb=" O   THR B 338 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE B 329 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    711 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      99 hydrogen bonds
      186 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 2.62 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2221
        1.34 -     1.45: 1911
        1.45 -     1.57: 4322
        1.57 -     1.69: 143
        1.69 -     1.81: 8
  Bond restraints: 8605
  Sorted by residual:
  bond pdb=" C5   DC D  77 "
       pdb=" C6   DC D  77 "
    ideal  model  delta    sigma   weight residual
    1.337  1.360 -0.023 2.00e-02 2.50e+03 1.37e+00
  bond pdb=" CG  PRO A 226 "
       pdb=" CD  PRO A 226 "
    ideal  model  delta    sigma   weight residual
    1.512  1.483  0.029 2.70e-02 1.37e+03 1.14e+00
  bond pdb=" CA  GLN B 332 "
       pdb=" C   GLN B 332 "
    ideal  model  delta    sigma   weight residual
    1.519  1.530 -0.011 1.01e-02 9.80e+03 1.09e+00
  bond pdb=" C   LEU B 149 "
       pdb=" N   PRO B 150 "
    ideal  model  delta    sigma   weight residual
    1.326  1.341 -0.015 1.44e-02 4.82e+03 1.08e+00
  bond pdb=" C   LEU A 149 "
       pdb=" N   PRO A 150 "
    ideal  model  delta    sigma   weight residual
    1.326  1.340 -0.014 1.44e-02 4.82e+03 9.61e-01
  ... (remaining 8600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 11952
        1.47 -     2.95: 155
        2.95 -     4.42: 60
        4.42 -     5.89: 2
        5.89 -     7.36: 1
  Bond angle restraints: 12170
  Sorted by residual:
  angle pdb=" N   VAL A 276 "
        pdb=" CA  VAL A 276 "
        pdb=" C   VAL A 276 "
      ideal   model   delta    sigma   weight residual
     113.20  109.76    3.44 9.60e-01 1.09e+00 1.29e+01
  angle pdb=" CA  LYS B  13 "
        pdb=" C   LYS B  13 "
        pdb=" N   PRO B  14 "
      ideal   model   delta    sigma   weight residual
     118.83  116.42    2.41 8.70e-01 1.32e+00 7.69e+00
  angle pdb=" N   TYR A 115 "
        pdb=" CA  TYR A 115 "
        pdb=" C   TYR A 115 "
      ideal   model   delta    sigma   weight residual
     111.07  108.19    2.88 1.07e+00 8.73e-01 7.24e+00
  angle pdb=" C2'   C C 134 "
        pdb=" C1'   C C 134 "
        pdb=" N1    C C 134 "
      ideal   model   delta    sigma   weight residual
     112.40  119.76   -7.36 3.00e+00 1.11e-01 6.02e+00
  angle pdb=" N   ARG A 307 "
        pdb=" CA  ARG A 307 "
        pdb=" C   ARG A 307 "
      ideal   model   delta    sigma   weight residual
     111.07  108.64    2.43 1.07e+00 8.73e-01 5.17e+00
  ... (remaining 12165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4602
       17.79 -    35.58: 289
       35.58 -    53.37: 120
       53.37 -    71.16: 87
       71.16 -    88.95: 27
  Dihedral angle restraints: 5125
    sinusoidal: 2372
      harmonic: 2753
  Sorted by residual:
  dihedral pdb=" N   GLU B 378 "
           pdb=" CA  GLU B 378 "
           pdb=" CB  GLU B 378 "
           pdb=" CG  GLU B 378 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.88   54.88     3      1.50e+01 4.44e-03 9.31e+00
  dihedral pdb=" O5'   U C 135 "
           pdb=" C5'   U C 135 "
           pdb=" C4'   U C 135 "
           pdb=" C3'   U C 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.00  122.72   52.28     3      1.50e+01 4.44e-03 9.10e+00
  dihedral pdb=" N   GLU B  79 "
           pdb=" CA  GLU B  79 "
           pdb=" CB  GLU B  79 "
           pdb=" CG  GLU B  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.51   50.51     3      1.50e+01 4.44e-03 8.91e+00
  ... (remaining 5122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1226
       0.045 -    0.091: 158
       0.091 -    0.136: 74
       0.136 -    0.181: 2
       0.181 -    0.227: 3
  Chirality restraints: 1463
  Sorted by residual:
  chirality pdb=" C1'   C C 134 "
            pdb=" O4'   C C 134 "
            pdb=" C2'   C C 134 "
            pdb=" N1    C C 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.23    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C3'  DT D  78 "
            pdb=" C4'  DT D  78 "
            pdb=" O3'  DT D  78 "
            pdb=" C2'  DT D  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.47   -0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" C3'  DG D  73 "
            pdb=" C4'  DG D  73 "
            pdb=" O3'  DG D  73 "
            pdb=" C2'  DG D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.48   -0.18 2.00e-01 2.50e+01 8.32e-01
  ... (remaining 1460 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 224 "    0.037 5.00e-02 4.00e+02   5.54e-02 4.91e+00
        pdb=" N   PRO A 225 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 225 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 225 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 257 "   -0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   ILE A 257 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE A 257 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 258 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D  78 "    0.010 2.00e-02 2.50e+03   7.34e-03 1.35e+00
        pdb=" N1   DT D  78 "    0.009 2.00e-02 2.50e+03
        pdb=" C2   DT D  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DT D  78 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3   DT D  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DT D  78 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT D  78 "    0.012 2.00e-02 2.50e+03
        pdb=" C5   DT D  78 "   -0.005 2.00e-02 2.50e+03
        pdb=" C7   DT D  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT D  78 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 984
        2.74 -     3.28: 8367
        3.28 -     3.82: 14066
        3.82 -     4.36: 15575
        4.36 -     4.90: 24636
  Nonbonded interactions: 63628
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 321 "
            pdb=" NZ  LYS B 385 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ARG A 211 "
            pdb=" NE  ARG A 211 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OG  SER A 105 "
            pdb=" OG  SER A 191 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ALA A 538 "
            pdb=" NZ  LYS A 540 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   TRP A 239 "
            pdb=" N   GLY A 316 "
     model   vdw
     2.302 3.120
  ... (remaining 63623 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.560
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8605  Z= 0.130
  Angle     :  0.500   7.364  12170  Z= 0.273
  Chirality :  0.039   0.227   1463
  Planarity :  0.003   0.055   1272
  Dihedral  : 17.215  88.947   3343
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.54 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  1.28 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.82 (0.23), residues: 926
  helix: -1.78 (0.24), residues: 325
  sheet: -4.65 (0.28), residues: 147
  loop : -3.82 (0.24), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 402 
 HIS   0.003   0.000   HIS A 208 
 PHE   0.006   0.001   PHE A 227 
 TYR   0.010   0.001   TYR B 354 
 ARG   0.002   0.000   ARG B 199 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 PHE cc_start: 0.9239 (t80) cc_final: 0.8991 (t80)
REVERT: A  366 LYS cc_start: 0.9720 (tppp) cc_final: 0.9463 (mptt)
REVERT: B   42 GLU cc_start: 0.9454 (tt0) cc_final: 0.9181 (tt0)
REVERT: B  206 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8939 (ttm170)
REVERT: B  307 ARG cc_start: 0.9207 (mtm180) cc_final: 0.8986 (mtt-85)
REVERT: B  320 ASP cc_start: 0.8915 (t0) cc_final: 0.8593 (t70)
REVERT: B  378 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9193 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2808
  time to fit residues: 37.5551
Evaluate side-chains
  55 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0970
   chunk 40 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN
A 475 GLN
B  57 ASN
B 161 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.060582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.049237 restraints weight = 63075.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.050333 restraints weight = 39992.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.050973 restraints weight = 28136.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8605  Z= 0.151
  Angle     :  0.533   8.011  12170  Z= 0.261
  Chirality :  0.038   0.146   1463
  Planarity :  0.004   0.064   1272
  Dihedral  : 18.384  87.120   2135
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.37 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.26), residues: 926
  helix: -0.28 (0.28), residues: 342
  sheet: -3.42 (0.38), residues: 119
  loop : -3.30 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 402 
 HIS   0.002   0.001   HIS B 235 
 PHE   0.009   0.001   PHE A 227 
 TYR   0.018   0.001   TYR B 146 
 ARG   0.007   0.001   ARG A 211 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9100 (ttm110) cc_final: 0.8548 (tpt90)
REVERT: B   42 GLU cc_start: 0.9471 (tt0) cc_final: 0.9254 (tt0)
REVERT: B  115 TYR cc_start: 0.8364 (m-80) cc_final: 0.7974 (m-80)
REVERT: B  138 GLU cc_start: 0.8657 (pp20) cc_final: 0.8004 (pp20)
REVERT: B  184 MET cc_start: 0.7634 (mmp) cc_final: 0.7347 (mmp)
REVERT: B  206 ARG cc_start: 0.9271 (mtp180) cc_final: 0.9059 (ttm170)
REVERT: B  320 ASP cc_start: 0.8932 (t0) cc_final: 0.8697 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2292
  time to fit residues: 22.1280
Evaluate side-chains
  51 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 85 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0770
   chunk 91 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.0140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 545 ASN
B 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.059046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.047387 restraints weight = 64147.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.048539 restraints weight = 38950.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.049348 restraints weight = 26563.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8605  Z= 0.144
  Angle     :  0.495   7.549  12170  Z= 0.240
  Chirality :  0.037   0.132   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.301  85.555   2135
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.28), residues: 926
  helix:  0.52 (0.29), residues: 343
  sheet: -2.81 (0.39), residues: 129
  loop : -2.75 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 402 
 HIS   0.001   0.000   HIS B 235 
 PHE   0.021   0.002   PHE B 416 
 TYR   0.011   0.001   TYR B 146 
 ARG   0.005   0.001   ARG B 143 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9032 (mmp) cc_final: 0.8754 (mmm)
REVERT: A  211 ARG cc_start: 0.9087 (ttm110) cc_final: 0.8565 (tpt90)
REVERT: B   41 MET cc_start: 0.8572 (mtm) cc_final: 0.8363 (mtt)
REVERT: B   42 GLU cc_start: 0.9445 (tt0) cc_final: 0.9220 (tt0)
REVERT: B  320 ASP cc_start: 0.8887 (t0) cc_final: 0.8614 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1888
  time to fit residues: 16.8294
Evaluate side-chains
  48 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    0.0970
   chunk 91 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0770
   chunk 50 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0770
   chunk 3 optimal weight:   20.0000
   overall best weight:    0.5896

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 545 ASN
B 145 GLN
B 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.058985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.046983 restraints weight = 57343.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.048117 restraints weight = 35355.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.048919 restraints weight = 24403.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8605  Z= 0.123
  Angle     :  0.485   7.755  12170  Z= 0.231
  Chirality :  0.037   0.138   1463
  Planarity :  0.004   0.061   1272
  Dihedral  : 18.164  81.464   2135
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.28), residues: 926
  helix:  0.88 (0.30), residues: 340
  sheet: -2.24 (0.40), residues: 137
  loop : -2.30 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 402 
 HIS   0.002   0.000   HIS A 208 
 PHE   0.008   0.001   PHE B 130 
 TYR   0.011   0.001   TYR A 188 
 ARG   0.003   0.000   ARG B 143 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9060 (mmp) cc_final: 0.8766 (mmm)
REVERT: A  180 ILE cc_start: 0.8536 (mt) cc_final: 0.8297 (pt)
REVERT: A  211 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8552 (tpt90)
REVERT: B   41 MET cc_start: 0.8764 (mtm) cc_final: 0.8423 (mtt)
REVERT: B  320 ASP cc_start: 0.8896 (t0) cc_final: 0.8613 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1906
  time to fit residues: 17.0211
Evaluate side-chains
  48 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 82 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 2 optimal weight:   10.9990
   chunk 46 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.054737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.043590 restraints weight = 65375.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.044562 restraints weight = 41258.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.045256 restraints weight = 28953.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8605  Z= 0.259
  Angle     :  0.577  11.492  12170  Z= 0.283
  Chirality :  0.037   0.151   1463
  Planarity :  0.004   0.059   1272
  Dihedral  : 18.588  91.104   2135
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.28), residues: 926
  helix:  0.70 (0.29), residues: 351
  sheet: -2.04 (0.42), residues: 130
  loop : -2.31 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 410 
 HIS   0.005   0.001   HIS B 235 
 PHE   0.021   0.002   PHE B 416 
 TYR   0.016   0.002   TYR B 146 
 ARG   0.007   0.001   ARG A 463 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9129 (ttm110) cc_final: 0.8648 (tpt90)
REVERT: B   41 MET cc_start: 0.8656 (mtm) cc_final: 0.8273 (mtt)
REVERT: B   42 GLU cc_start: 0.9418 (tt0) cc_final: 0.8894 (tp30)
REVERT: B  320 ASP cc_start: 0.8805 (t0) cc_final: 0.8448 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1787
  time to fit residues: 13.9756
Evaluate side-chains
  40 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    0.0070
   chunk 64 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    0.9804

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.055880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.044744 restraints weight = 64524.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.045755 restraints weight = 40228.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.046453 restraints weight = 28060.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8605  Z= 0.132
  Angle     :  0.498   7.891  12170  Z= 0.236
  Chirality :  0.036   0.137   1463
  Planarity :  0.004   0.061   1272
  Dihedral  : 18.320  83.368   2135
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.28), residues: 926
  helix:  1.03 (0.30), residues: 349
  sheet: -1.81 (0.43), residues: 131
  loop : -2.10 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 402 
 HIS   0.002   0.000   HIS A 208 
 PHE   0.012   0.001   PHE B 416 
 TYR   0.009   0.001   TYR A 501 
 ARG   0.002   0.000   ARG B 143 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9128 (ttm110) cc_final: 0.8562 (tpt90)
REVERT: B   41 MET cc_start: 0.8671 (mtm) cc_final: 0.8330 (mtt)
REVERT: B   42 GLU cc_start: 0.9480 (tt0) cc_final: 0.8972 (mm-30)
REVERT: B  320 ASP cc_start: 0.8790 (t0) cc_final: 0.8537 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1611
  time to fit residues: 13.0745
Evaluate side-chains
  45 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.056452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.045144 restraints weight = 64567.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.046188 restraints weight = 39951.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.046931 restraints weight = 27663.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8605  Z= 0.120
  Angle     :  0.493   8.051  12170  Z= 0.231
  Chirality :  0.036   0.133   1463
  Planarity :  0.004   0.061   1272
  Dihedral  : 18.169  80.186   2135
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.29), residues: 926
  helix:  1.15 (0.30), residues: 350
  sheet: -1.54 (0.44), residues: 131
  loop : -1.95 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 402 
 HIS   0.002   0.000   HIS A 208 
 PHE   0.009   0.001   PHE A 227 
 TYR   0.010   0.001   TYR B 146 
 ARG   0.003   0.000   ARG B 143 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8748 (mtm) cc_final: 0.8353 (mtt)
REVERT: B   42 GLU cc_start: 0.9449 (tt0) cc_final: 0.9004 (mm-30)
REVERT: B  184 MET cc_start: 0.8150 (mmp) cc_final: 0.7901 (mmp)
REVERT: B  320 ASP cc_start: 0.8801 (t0) cc_final: 0.8520 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1472
  time to fit residues: 11.9800
Evaluate side-chains
  44 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.053511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.042263 restraints weight = 66727.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.043290 restraints weight = 40349.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.044020 restraints weight = 27841.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8605  Z= 0.231
  Angle     :  0.557   9.257  12170  Z= 0.273
  Chirality :  0.037   0.144   1463
  Planarity :  0.004   0.062   1272
  Dihedral  : 18.461  85.969   2135
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.29), residues: 926
  helix:  1.05 (0.30), residues: 354
  sheet: -1.62 (0.40), residues: 148
  loop : -1.93 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 398 
 HIS   0.005   0.001   HIS B 235 
 PHE   0.018   0.002   PHE B 416 
 TYR   0.016   0.002   TYR B 146 
 ARG   0.003   0.000   ARG B 143 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8743 (mtm) cc_final: 0.8343 (mtt)
REVERT: B   42 GLU cc_start: 0.9376 (tt0) cc_final: 0.8934 (mm-30)
REVERT: B  320 ASP cc_start: 0.8752 (t0) cc_final: 0.8420 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1514
  time to fit residues: 10.9613
Evaluate side-chains
  36 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 91 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0270
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.7442

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.055277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.043948 restraints weight = 65794.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.044997 restraints weight = 40556.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.045729 restraints weight = 28139.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8605  Z= 0.129
  Angle     :  0.508   8.111  12170  Z= 0.242
  Chirality :  0.037   0.144   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.252  81.849   2135
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.29), residues: 926
  helix:  1.34 (0.30), residues: 344
  sheet: -1.37 (0.42), residues: 147
  loop : -1.72 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 398 
 HIS   0.001   0.000   HIS A 208 
 PHE   0.009   0.001   PHE A 227 
 TYR   0.008   0.001   TYR A 501 
 ARG   0.003   0.000   ARG B 125 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 PHE cc_start: 0.9047 (t80) cc_final: 0.8747 (t80)
REVERT: B   41 MET cc_start: 0.8755 (mtm) cc_final: 0.8309 (mtt)
REVERT: B   42 GLU cc_start: 0.9425 (tt0) cc_final: 0.8985 (mm-30)
REVERT: B  124 PHE cc_start: 0.9327 (t80) cc_final: 0.9086 (t80)
REVERT: B  320 ASP cc_start: 0.8808 (t0) cc_final: 0.8514 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1580
  time to fit residues: 12.2856
Evaluate side-chains
  44 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B 137 ASN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.049965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.039180 restraints weight = 68419.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.040075 restraints weight = 43486.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.040716 restraints weight = 31032.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075   8605  Z= 0.442
  Angle     :  0.740  12.902  12170  Z= 0.372
  Chirality :  0.041   0.200   1463
  Planarity :  0.005   0.062   1272
  Dihedral  : 19.064  94.010   2135
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.27), residues: 926
  helix:  0.67 (0.29), residues: 340
  sheet: -1.46 (0.43), residues: 141
  loop : -2.17 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 426 
 HIS   0.009   0.002   HIS B 235 
 PHE   0.040   0.003   PHE B 160 
 TYR   0.030   0.003   TYR A 127 
 ARG   0.005   0.001   ARG A 307 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8753 (mtm) cc_final: 0.8416 (mtt)
REVERT: B   42 GLU cc_start: 0.9309 (tt0) cc_final: 0.8836 (mm-30)
REVERT: B   60 VAL cc_start: 0.9690 (t) cc_final: 0.9245 (m)
REVERT: B  130 PHE cc_start: 0.8856 (p90) cc_final: 0.8641 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1496
  time to fit residues: 9.2087
Evaluate side-chains
  34 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 97 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 82 optimal weight:    8.9990
   chunk 16 optimal weight:    0.1980
   chunk 5 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   overall best weight:    0.6482

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.053734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.042384 restraints weight = 65177.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.043397 restraints weight = 40481.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.044107 restraints weight = 28342.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8605  Z= 0.133
  Angle     :  0.538   8.018  12170  Z= 0.257
  Chirality :  0.037   0.143   1463
  Planarity :  0.004   0.059   1272
  Dihedral  : 18.424  82.464   2135
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.29), residues: 926
  helix:  1.21 (0.30), residues: 348
  sheet: -1.07 (0.44), residues: 136
  loop : -1.85 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 229 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.009   0.001   PHE A 227 
 TYR   0.010   0.001   TYR B 146 
 ARG   0.003   0.001   ARG B 125 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2146.79 seconds
wall clock time: 38 minutes 22.95 seconds (2302.95 seconds total)